Can we regard file-system structure as one part of architecture?

Question

Put this image inside images folder. All JavaScript files should go inside a folder called js. Put templates inside a folder called site-templates and for each template, have three folders called layouts, looks, and pages.

We're all familiar with these file-system structures in which we try to logically and efficiently categorize files and folders in an acceptable hierarchy inside our projects. On the other hand, because many times we do I/O operations on these files, changing the file-system structure forces us to update parts of our code, no matter how high-tech, and decoupled our code is.

My question is, based on the effect that a file-system structure has on an overall project, can we consider it as a part of the software architecture? Because, in many cases, choosing a correct file-system structure prevents us from duplicating a file, say jQuery, in many places.